Mercurial > repos > lecorguille > xcms_plot_chromatogram

annotate test-data/faahKO-single.xset.merged.group.retcor.group.fillpeaks.summary.html @ 16:9291271ec4d9 draft default tip

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planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 95721ced8347c09e79340e6d67ecb41c5cc64163
author workflow4metabolomics
date Mon, 03 Feb 2025 14:46:19 +0000
parents 8846a03995d3
children
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14
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1 <!DOCTYPE html>
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2 <HTML lang='en'>
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3 <HEAD>
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4 <meta http-equiv='Content-Type' content='text/html; charset=UTF-8' />
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5 <title>[W4M] XCMS analysis summary</title>
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6 <style>
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7 table, tr, td, th { border: 1px solid #000000; border-collapse:collapse; }
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8 td, th { padding: 5px; padding-right: 12px; }
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9 th { background: #898989; text-align:left;color: white;}
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10 h2 { color: #FFA212; }
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11 ul li { margin-bottom:10px; }
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12 </style>
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13 </HEAD>
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14 <BODY>
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15 <div><h1>___ XCMS analysis summary using Workflow4Metabolomics ___</h1>
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16 By: planemo@galaxyproject.org -
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17 Date: 230525-08:53:25
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18 </div>
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19 <h2>Samples used:</h2>
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20 <div><table>
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21 <tr><th>sample</th><th>filename</th></tr>
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22 <tr><td>ko15</td><td>ko15.CDF</td></tr><tr><td>ko16</td><td>ko16.CDF</td></tr><tr><td>wt15</td><td>wt15.CDF</td></tr><tr><td>wt16</td><td>wt16.CDF</td></tr>
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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23 </table>
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24
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25 </div>
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26 <h2>Function launched:</h2>
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27 <div><table>
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28 <tr><th>timestamp<sup>***</sup></th><th>function</th><th>argument</th><th>value</th></tr>
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29 <tr><td>Mon May 11 09:37:30 2020</td><td>Peak detection</td><td colspan='2'><pre>
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30 Object of class: CentWaveParam
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31 Parameters:
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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32 ppm: 25
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33 peakwidth: 20, 50
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34 snthresh: 10
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35 prefilter: 3, 100
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36 mzCenterFun: wMean
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37 integrate: 1
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38 mzdiff: -0.001
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39 fitgauss: FALSE
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40 noise: 0
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41 verboseColumns: FALSE
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42 roiList length: 0
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43 firstBaselineCheck TRUE
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44 roiScales length: 0
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45 </pre></td></tr>
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46 <tr><td>Mon May 11 09:37:49 2020</td><td>Peak grouping</td><td colspan='2'><pre>
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47 Object of class: PeakDensityParam
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48 Parameters:
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49 sampleGroups: character of length 4
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50 bw: 5
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51 minFraction: 0.3
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52 minSamples: 1
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53 binSize: 0.01
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54 maxFeatures: 50
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55 </pre></td></tr>
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56 <tr><td>Mon May 11 09:38:08 2020</td><td>Retention time correction</td><td colspan='2'><pre>
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57 Object of class: PeakGroupsParam
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58 Parameters:
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59 minFraction: 0.85
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60 extraPeaks: 1
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61 smooth: loess
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62 span: 0.2
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63 family: gaussian
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64 subset:
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65 number of peak groups: 53
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66 </pre></td></tr>
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67 <tr><td>Mon May 11 09:38:09 2020</td><td>Peak grouping</td><td colspan='2'><pre>
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68 Object of class: PeakDensityParam
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69 Parameters:
8846a03995d3 planemo upload for repository https://github.com/workflow4metabolomics/tools-metabolomics/ commit 2cb157bd9a8701a3d6874e084032cbd050b8953e
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70 sampleGroups: character of length 4
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71 bw: 20
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72 minFraction: 0.4
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73 minSamples: 1
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74 binSize: 0.25
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75 maxFeatures: 50
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76 </pre></td></tr>
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77 <tr><td>Mon May 11 09:38:18 2020</td><td>Missing peak filling</td><td colspan='2'><pre>
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78 Object of class: FillChromPeaksParam
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79 Parameters:
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80 expandMz: 0
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81 expandRt: 0
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82 ppm: 0
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83 </pre></td></tr>
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84 </table>
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85 <br/><sup>***</sup>timestamp format: DD MM dd hh:mm:ss YYYY or yymmdd-hh:mm:ss
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86 </div>
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87 <h2>Informations about the XCMSnExp object:</h2>
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88 <div><pre>
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89 MSn experiment data ("XCMSnExp")
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90 Object size in memory: 1.55 Mb
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91 - - - Spectra data - - -
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92 MS level(s): 1
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93 Number of spectra: 5112
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94 MSn retention times: 41:38 - 75:7 minutes
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95 - - - Processing information - - -
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96 Data loaded [Mon May 11 09:37:30 2020]
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97 MSnbase version: 2.10.1
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98 - - - Meta data - - -
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99 phenoData
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100 rowNames: 1 2 3 4
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101 varLabels: sample_name sample_group
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102 varMetadata: labelDescription
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103 Loaded from:
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104 [1] ko15.CDF... [4] wt16.CDF
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105 Use 'fileNames(.)' to see all files.
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106 protocolData: none
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107 featureData
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108 featureNames: F1.S0001 F1.S0002 ... F4.S1278 (5112 total)
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109 fvarLabels: fileIdx spIdx ... spectrum (31 total)
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110 fvarMetadata: labelDescription
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111 experimentData: use 'experimentData(object)'
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112 - - - xcms preprocessing - - -
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113 Chromatographic peak detection:
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114 method: centWave
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115 15405 peaks identified in 4 samples.
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116 On average 3851 chromatographic peaks per sample.
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117 Alignment/retention time adjustment:
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118 method: peak groups
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119 Correspondence:
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120 method: chromatographic peak density
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121 6349 features identified.
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122 Median mz range of features: 0
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123 Median rt range of features: 0
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124 6154 filled peaks (on average 1538.5 per sample).
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125 </pre></div>
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126 <h2>Informations about the xcmsSet object:</h2>
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127 <div><pre>
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128 An "xcmsSet" object with 4 samples
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129
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130 Time range: 2509.2-4481.8 seconds (41.8-74.7 minutes)
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131 Mass range: 200.1-600 m/z
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132 Peaks: 15405 (about 3851 per sample)
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133 Peak Groups: 6349
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134 Sample classes: KO, WT
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135
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136 Feature detection:
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137 o Peak picking performed on MS1.
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138 o Scan range limited to 1 - 1278
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139 Profile settings: method = bin
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140 step = 0.1
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141
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142 Memory usage: 3.98 MB
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143 </pre></div>
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144 <h2>Citations:</h2>
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145 <div><ul>
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146 <li>To cite the <b>XCMS</b> package in publications use:
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147 <ul>
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148 <li>Smith, C.A. and Want, E.J. and O'Maille, G. and Abagyan,R. and Siuzdak, G.XCMS: Processing mass spectrometry data for metabolite profiling using nonlinear peak alignment, matching and identification, Analytical Chemistry, 78:779-787 (2006)</li>
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149 <li>Ralf Tautenhahn, Christoph Boettcher, Steffen Neumann: Highly sensitive feature detection for high resolution LC/MS BMC Bioinformatics, 9:504 (2008)</li>
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150 <li>H. Paul Benton, Elizabeth J. Want and Timothy M. D. Ebbels Correction of mass calibration gaps in liquid chromatography-mass spectrometry metabolomics data Bioinformatics, 26:2488 (2010)</li>
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151 </ul>
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152 </li>
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153 <li>To cite the <b>CAMERA</b> package in publications use:
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154 <ul>
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155 <li>Kuhl, C., Tautenhahn, R., Boettcher, C., Larson, T. R. and Neumann,S. CAMERA: an integrated strategy for compound spectra extraction and annotation of liquid chromatography/mass spectrometry data sets. Analytical Chemistry, 84:283-289 (2012)</li>
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156 </ul>
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157 </li>
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158 <li>To cite the <b>Workflow4Metabolimics (W4M)</b> project in publications use:
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159 <ul>
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160 <li>Franck Giacomoni, Gildas Le Corguillé, Misharl Monsoor, Marion Landi, Pierre Pericard, Mélanie Pétéra, Christophe Duperier, Marie Tremblay-Franco, Jean-François Martin, Daniel Jacob, Sophie Goulitquer, Etienne A. Thévenot and Christophe Caron (2014). Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics. Bioinformatics doi:10.1093/bioinformatics/btu813</li>
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161 </ul>
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162 </li>
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163 </ul></div>
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164 </BODY>
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165 </HTML>